Yet Another Pulsar Processor (YAPP) 3.7-beta

README

Yet Another Pulsar Processor (YAPP) is a suite of radio pulsar data analysis software.

The YAPP tools available with this release are:

• yapp_viewmetadata : Prints metadata to standard output.
• yapp_viewdata : Plots data to PGPLOT device.
• yapp_ft : Performs PFB/FFT on 8-bit, complex, dual-pol. baseband data.
• yapp_dedisperse : Dedisperses filterbank format data.
• yapp_decimate : Decimates filterbank and time series data.
• yapp_smooth : Boxcar-smoothes dedispersed time series data.
• yapp_filter : Processes dedispersed time series data with a custom frequency-domain filter.
• yapp_add : Coherently add dedispersed time series data from multiple frequency bands.
• yapp_fold : Folds filterbank and dedispersed time series data.
• yapp_subtract : Subtracts two dedispersed time series files.
• yapp_siftpulses : Sifts multiple dedispersed time series files for bright pulses.
• yapp_stacktim : Stacks time series data to form filterbank data.
• yapp_split : Splits time series data into time sections.
• yapp_showinfo : Displays supported file types and colourmaps.

YAPP also comes with the following utilities:

• yapp_fits2fil : Converts PSRFITS to SIGPROC .fil.
• yapp_fil2h5 : Converts SIGPROC .fil to HDF5.
• yapp_dat2tim : Converts PRESTO '.dat' to SIGPROC .tim.
• yapp_tim2dat : Converts SIGPROC '.tim' to PRESTO .dat.
• yapp_ym2fil : Converts YAPP Metadata to SIGPROC filterbank header format.

YAPP includes the following scripts:

• yapp_genpfbcoeff.py : Generate PFB pre-filter co-efficients for yapp_ft.
• yapp_genfiltermask.py : Generate filter response for yapp_filter.
• yapp_calcspecidx.py : Calculate spectral index from a sequence of time series files corresponding to multiple bands.
• yapp_stackprof.py : Stacks folded profiles from multiple bands to show a plot of phase versus frequency.
• yapp_addprof.py : Add [calibrated] profiles from two polarisations.
• yapp_viewcand.rb : Converts prepfold candidate plots in PS format to PNG, and generates a set of HTML pages displaying a tiled set of plots.
• yapp_subbanddedisperse.rb : Creates a sub-band-dedispersed filterbank file from a raw filterbank file and optionally does smoothing.
• yapp_replacemetadata.rb : Replaces header in a SIGPROC .fil file with user-supplied header.

The supported file formats are SIGPROC .fil and SIGPROC .tim, with limited support for DAS .spec and .dds, PSRFITS, PRESTO .dat, and HDF5. Not all programs support all file formats.

For detailed usage instructions, refer the man pages or online documentation.

System requirements

Linux/OS X, a C compiler, PGPLOT with C binding, FFTW3, CFITSIO, and optionally, HDF5, Python with NumPy and Matplotlib, Ruby, and ImageMagick.

Installation instructions

Standard

Firstly, clone this repository.

git clone https://github.com/jayanthc/yapp.git

On a typical Ubuntu-based machine in which PGPLOT, FFTW3, and CFITSIO were installed via APT, and the optional HDF5 was installed in its default location, running make (or make HDF5=yes), optionally followed by sudo make install, should work, with the binaries being copied to /usr/local/bin. For different operating systems and/or different PGPLOT/FFTW3/CFITSIO/HDF5 installation directories and/or a different choice of YAPP installation directory, the makefile may need to be modified by hand. YAPP scripts require YAPP binaries to be in the search path.

cd yapp
make # 'make HDF5=yes' if you would like HDF5 support
sudo make install

Using Docker

YAPP can be installed and run using Docker, as shown below. To install:

docker build -t yapp https://raw.githubusercontent.com/jayanthc/yapp/release/Dockerfile

To run YAPP with graphics, the X server on the host needs to be made available to the container. The easiest way to use YAPP with graphics is to run the script runYAPPOnDocker.sh, which will run the container, mounting a data volume of your choice to /data, and provide a terminal to work on that data. An example is given below.

./runYAPPOnDocker.sh
YAPP:/$ yapp_viewdata /data/test.fil
...
YAPP:/$ yapp_dedisperse -d 100 /data/test.fil
...
YAPP:/$ yapp_decimate -t 1024 /data/test.dm100.fil
...
YAPP:/$ exit # exit when done

You will need to modify runYAPPOnDocker.sh to specify your data directory, and if your Ethernet interface is not en0. Note that if your host operating system is Linux, replace en0 with eth0 (or whatever interface is appropriate). runYAPPOnDocker.sh has not been tested on Linux hosts.

Created by Jayanth Chennamangalam
http://jayanthc.github.io/yapp/